Friday, January 29, 2010

Host Terry Gross talks with journalist Mark Schapiro who does a really excellent job of explaining what a cap and trade is, how it works and the derivative markets it has spawned.

Top Questions: ....would you explain what the market is..and what people are actually buying and selling...

... explain a little more how investors make money out of the carbon trading..

The similarity between the housing derivatives and carbon derivatives are eerily similar and unnerving....carbon offsets from different projects with different standards of reliabilty in terms of their future ability to actually reduce emissions being grouped into say one million ton bundles and sold on the derivatives markets.

At least for the European markets where carbon cap and trade has been going on for some time the actual amount of emissions reductions from cap and trade schemes has been below expectations according to Mr Schapiro.

Monday, January 25, 2010

Bookstores in Pune don't have a big science section. I wandered into Crosswords yesterday and found the science section almost bare.

It was mostly filled with large picture books, some travel books and a few major titles.

Richard Dawkins new book on evolution The Greatest Show On Earth was on the shelf... But what is that book below it.... The Selfless Gene..? I thought his other famous book was the Selfish Gene...

...never mind.... that is The Selfless Gene by Charles Foster. What an odd title to stock given the plethora of choices..

During my graduate and work days in the U.S. the big bookstore was a kind of a refuge for me after work. Evening scrabble with friends and browsing through Economist and Scientific American saw many evenings through.

My buying method has been to browse books in bookstores and then on online and buy what I like. Usually in bulk. Hey now...that wasn't unethical was it..?.... the spectacular amounts of coffee and hot chocolate I drank at the bookstore cafe more than made up for my lack of buying books there...

I haven't been spending any time at all in book stores in Pune.

The science section is poor and the cafe which served good coffee and yummy chocolate cakes shut down at Crosswords some time back.

Thursday, January 21, 2010

[Update :New geochemical and geomorphological studies strongly suggest that Yamuna and Sutlej stopped flowing in to the Ghaggar /Saraswati thousands of years before the Harappan civilization. See these posts for more on this topic -

A number of recent studies have bolstered the case that the River Ghaggar - which has been equated with the River Saraswati described in the Rigveda - did not have a glacial source in historical times and was likely always fed from the sub Himalayas (Siwaliks).

Why is this of any interest?

The background is the controversial question of the origin of the Aryans.

The more widely accepted theory is that proto-Sanskrit speakers entered the northwestern parts of India after or during the latter stages of the demise of the Harappan city states beginning around 1800 -1500 B.C. The ancestors of these proto-Sanskrit speakers can be traced according to this theory to the central Asia steppes. In terms of the local ecology, geological evidence shows that by this time the River Ghaggar which was once a river with substantial water flow and was perhaps perennial had transformed into a smaller ephemeral stream.

The competing theory is that the Aryans are indigenous to India - indigenous in the sense that they were present on the northwestern plains at least since the advent of agriculture. In this scenario the Harappan city states was an Aryan civilization. To support this more ancient presence of the Aryans on the plains of Haryana, Punjab and Rajasthan, one line of argument is to point to the Rigveda which mentions a mighty Saraswati river located between the rivers Sutlej and the Yamuna. The argument is that the composers of the Rigveda must have been living on the plains of Haryana when the Ghaggar = Saraswati was perennial which means before 1800 B.C which in one way supports the theory that they and the Harappan people were one and the same.

The Rigveda describes the Saraswati as originating high in the Himalayas. It is described as a mighty river and so has been thought to have been perennial and having a glacial source. But today the Ghaggar / Saraswati is no doubt fed from only the Siwaliks, nowhere near the high glaciers. To account for this, supporters say that earlier the glacially fed Sutlej and /or Yamuna flowed into the Saraswati. Later around 1800 B.C or so the channels shifted and the Ghaggar was stranded as a small ephemeral Siwalik fed river. Image below shows the Ghaggar basin flanked by the Sutlej and Yamuna.

A virtual industry dedicated to creating geological scenarios as to how this must have happened and to collecting "evidence" has proliferated on the internet, in various articles and in popular books.

A review of the peer reviewed geological literature shows that these scenarios are wrong and are based on exaggerations of the size of the Ghaggar and misunderstandings of geological processes. I have written an explanation of much of the list below in an article for the magazine Pragati. A short list is given here.

1) Use of isotopes in search of Lost River - Journal of Radioanalytical and Nuclear Chemistry: Data on stable isotopes of water in buried channels of ancient Ghaggar in Rajasthan shows a composition compatible with water from Siwaliks and not glacial high Himalayas.

I say it is time to abandon the theory that Ghaggar/Saraswati had a glacial source in historical times.

That does not mean abandoning the broader theory that the Aryan /Vedic people were present on the Haryana plains before the collapse of the Harappan civilization. Archaeology and linguistics and perhaps genetics are a more powerful tool to address that question. Let me add here that most archaeologists and linguists support the theory that the Aryans were late arrivals to the northwestern part of India.

The funny thing is, in my opinion the theory of a glacial source of Saraswati is not necessary in this debate. The Ghaggar was a wetter river before 1800 B.C. because of a generally more wetter climate. Strong summer monsoons over the Siwaliks and then spring flow would have made human settlements along its banks sustainable. A life sustaining river would have been holy to the people depending on it, regardless of whether it had a glacial origin or not.

The insistence that there was a past glacial source derives from a belief that the Rigveda is accurate in every aspect of its recording of geography and physical events. Descriptions of Saraswati in Rigvedic hymns as originating from Heaven...High Mountains..boundless....impetuous...fast flowing.. arising from a slowly moving serpent Ahi (source here) has led to a conviction that the Saraswati arose from glaciers. This reading of the Rigveda has led to the theory being proposed initially and for sustaining it.

Unhappily for science and for those who are looking for a scientifically accurate account, this has frustratingly meant a popularization and easy availability through the internet of an increasingly untenable and unsupported geological narrative which is creeping into the public consciousness as the correct story. People who are supporting the glacial origin theory assert that they are approaching the problem as a scientific question and with a scientific temperament. I would like to take them at face value.

However, that does come with a condition and this is the willingness to give up on your pet theory if the evidence piles up against it. This is one of the critical tests of the scientific temperament. There is plenty to show now that the Ghaggar / Saraswati was always a Siwalik fed river. Persisting with the glacial theory in light of this gathering evidence and pointing to scripture as a back-up will diminish the scientific credibility of the "early Aryan presence" supporters and perpetuate misinformation about the subject. I hope one of them stands up and admits that geological data does not support this particular theory.

Almost 50 million years ago, the Greater Indian plate collided with the Eurasian plate leading to the formation of the mighty range. Usually, when two continental plates collide, the movement of the two plates stop. That did not happen with the Indian-Eurasian convergence.

The two plates continue to rub against each other generating stress, which is later released as earthquakes. An international team has now offered an explanation. In Sunday’s edition of “Nature Geoscience,” they suggest an internal mechanism that creates the drag which pulls the Indian plate towards its boundary with Eurasia.

“The India-Asia convergence cannot be explained by plate tectonics theory, which is deeply challenged,” said team leader Fabio Antonio Capitanio, a geoscientist at the University of Monash, Australia.

I don't have access to the full paper but from the abstract I gathered that the research uses estimates of the density of the Indian lithosphere and then models the forces prevalent in the India-Asia convergent zone. The Indian lithosphere has delaminated at the convergence zone. The upper crust has been scraped off and has been stacked into the Himalayan frontal ranges. The lower continental slab is denser than the underlying mantle and sinks into the mantle providing the necessary drag that explains the continued convergence at the collision zone.

The schematic below show the major tectonic faults across the India- Asia collisional zone. The lower part of the figure is at best speculative and shows the Indian plate subducting underneath the Asian plate but until recently not much was really known about the nature, structure and extent of this subduction.

What this study suggests is that the traditional plate tectonics forces of ridge push and slab pull that are drivers of plate motion may have diminishing influence on convergence at late stages of plate convergence. Continental crust is lighter than the mantle and in continent continent collision zones crustal buoyancy should be putting the brakes on subduction and convergence. Instead the model results suggest that internally generated forces driven by density differences at the site of the collision may be providing the necessary force to drive convergence.

Its an interesting result but I have to say I find Dr. Capitanio comment that plate tectonic theory is "deeply challenged" a bit hyperbolic.

You can think of an analogy from biology where a structure, trait,
feature and so on can be explained at two levels. A proximate
explanation may include the immediate physiological or mechanical causes but
there is a higher level ultimate explanation which is based on
evolution.

I don't think geoscientists seek a proximate explanation using plate tectonic theory for every aspect of Himalayan tectonics and structure. For example the great relief of the Himalayan ranges and some internal folded structures are best explained using concepts of vertical movements of crustal blocks driven by denudational isostasy. This means that continents bob up in response to unloading or removal of overlying mass by erosion.

For the Himalayan ranges there may be many proximate explanations. Isostasy and in this case if the models are correct internal density differences which is dragging the Indian continental slab down. But it is plate tectonics that has created these conditions in the first place. It is in a sense the ultimate explanation.

The key here is the phrase continued convergence. The India-Asia plate convergence zone has a long history. Convergence initially involved interaction of oceanic crust with oceanic crust, then as one oceanic crust was consumed by subduction, it was ocean crust with continental crust and finally the big Wham! Continental crust on both the Indian and Asian plates colliding. A recent study published in Science which seismically imaged the deep crustal and mantle roots of the Himalayas across the India-Asia collision zone found that the Indian plate has slid about 450 km underneath the Tibetian (Asian) plate and the upper mantle appears to shear off and sink. For most of this history conventional plate tectonic forces of ridge push and slab pull can explain the convergence.

It is in the latter mature stages of continent continent collision that this new study finds a role for autochthonous mechanisms.

Most people rightly tend to think of the Great Barrier Reef as a living wonder. But the current living ecosystem, the coral communities and associated faunal and floral assemblages have been built on a foundation of a community of dead corals. And that ancient community when it was living grew on a foundation on an earlier community and so on.. for hundreds of thousands of years through many episodes of community growth and decline and growth again.

This study delves into the mineralogical and geochemical transformations (Diagenesis) that occur in these reefs when sea-level fell and exposed the sea bed and the coral communities to fresh water.

As is the case with diagenetic research a lot of the base data is collected from micro scale analysis and this study does a detailed job. Cement mineralogy, (chemical precipitates) morphology, habits and associations are carefully documented. Textural features such as solution fabrics and pore space types are noted. The overall conclusion is that during sea-level fall meteoric (fresh water) aquifers developed in the exposed layers and there was considerable amounts of reaction of the coral skeleton with fresh water leading to destruction of minerals like aragonite and high Mg calcite and precipitation of low Mg calcite.

Based on these diagenetic textures distinct vadose zone (soil profile above the water table) and phreatic zone (below water table) demarcations are recognized in these ancient aquifers and some units show evidence of the water table being mobile i.e. migration up and down likely due to changing rainfall conditions.

That's the micro-level stuff and its a well characterized in this study.

My interest in diagenesis tends to make me look at the larger basin scale picture and I found much to think about in this paper. Diagenesis occurs during the establishment of large scale hydrologic systems in sediments and rocks. The scale and geometry of these hydrologic systems controls the extent and 3-D shape of alteration of the sediment.

Such thinking in terms of diagenetic reaction fronts, shapes and volumes is very important because these altered volumes of sediment may due to their properties of porosity and permeability act later in the sediment history as pathways and reservoirs for hydrocarbons and other economically important minerals like copper, lead and zinc.

Although not looked at from such an economic angle this study does recognize the larger controls on the development of hydrologic systems during sea-level falls.

One important diagenetic pattern revealed was that the fresh water reactions that took place cannot be tied to any particular emergent event although aquifer formation likely affected only the youngest deposition unit. This conclusion is based on the observation that there is no superimposition of diagenetic textures and cements.

This is a bit tricky. Say during a sea-level fall a particular depositional unit experiences meteoric diagenesis and then sea-level rises and drowns that unit. A new coral community will grow on that surface and form a younger depositional unit. Later sea-level falls again. Another fresh water aquifer develops. If it is thick enough it will affect not only the youngest sediment unit but the ones underlying it. So the older depositional units might then contain evidence of more than one generation of diagenetic products, a superimposition of events.

That kind of evidence of superimposition is lacking in these reefal units, leading the authors to conclude that the meteoric aquifers that formed were thin and did not penetrate deeper into the sequence.

The major reason for this is the lay of the land and the location of the reefal bodies in the context of the Australian shelf. The Barrier Reef is located some distance away from the Australian mainland and away from any continental relief. During sea-level falls the undulating topography of the reef, made up of mounds and depressions would have meant that the reefs would have been exposed as a chain of islands.

The depth to which groundwater circulates in these exposed islands i.e. the thickness of fresh water lenses under these islands is governed by the width of the islands, the hydrologic conductivity of the sediment and the amount of recharge. These relationships observed in several Holocene islands suggest a meteoric lens thickness of just 1% of island width.

This contrasts with carbonates sequences which accumulate as bodies fringing continental land masses with coastal relief. Here during sea level falls, the hinterland relief provides a stronger hydraulic head for fresh water to flow towards and into the exposed sea bed and circulate deeper into the sediment layers, generating diagenetic reaction zones which cut across depositional units.

One consequence of the thin meteoric lenses that episodically developed during the Barrier Reef history is that much of the sediment remained only partially altered. This is indicated not just by the sporadic presence of mineral aragonite which usually dissolves in fresh water, but by a cross plot of the oxygen and carbon isotopes of coral skeletal material in which the overall pattern of fresh water sediment interaction is brought out beautifully.

Here is the theory. Meteoric water is enriched in the lighter isotopes compared with sea water and compared with marine carbonate sediment. Imagine a marine carbonate sediment body reacting with meteoric (fresh) water. Marine carbonate is the dominant reservoir of carbon relative to meteoric water (means there is much more dissolved carbon in marine water than in fresh water) and thus the carbon composition of pore fluids quickly reaches a state of equilibrium with dissolving marine carbonate during water-rock interaction. So any product precipitated from this pore fluid will have the signature of marine carbon. In contrast, meteoric water is the main oxygen reservoir, and thus the oxygen composition of pore fluids with change towards a marine signature only after prolonged interaction with the isotopically heavier marine carbonate.

A pattern of relatively invariant oxygen and variable carbon is thus indicative of less water rock interaction during diagenesis.

That's what the bulk of data points of the key units in the above graph is pointing to. Here units 1, 9 and 2 are mostly marine and are not altered much by meteoric diagenesis. In the rest of the units the bulk of the samples show a constrained oxygen isotope signal (compared to total range of 0 - 9.5 parts per thousand) and a very variable carbon isotope signal. The depleted but constrained oxygen isotope values suggest that the
pore fluid composition were not impacted much by marine oxygen implying
limited reaction with rock as does the variable carbon which would have
been quickly acquired a uniform marine signature if water rock reactions had
been prolonged.

All this is because of thin discontinuous meteoric lenses and thick vadose profiles where diagenesis is concentrated in pockets and along very thin reaction fronts leaving other pockets of the sediment body unaltered.

Enjoyed the paper. It's a good mix of micro-scale detailed work on cements and geochemistry but done in a way that allows you to draw a larger picture of the controls that landscape, platform geometry and hydrologic systems exert on diagenesis.

....BWSSB (Bangalore Water Supply and Sewage Board) has installed bulk flow meters to monitor the flow of water in different areas and to check the wastage of water.

The board is expecting that GIS will help the department in checking the unaccounted for water. BWSSB has undertaken two major pilot projects to study the feasibility of implementing the system. The first of the two is expected to help the department, trace the leakage in the city through satellite imagery.

That's it.....the press release does not explain how.

Which means that lots of people not familiar with how imagery is collected and used will think that a water leak leaves a particular signature that can be recognized in a satellite image and that's how the Bangalore city government is going to keep a tab on leakages.

But that's not how it works. The pipes are buried under asphalt and concrete. For most GIS applications, satellite sensors which image in the visible and near infrared wavelengths are used to collect earth information. These wavelengths cannot penetrate the ground and image the buried water pipes. Even if there are lengths where pipes are exposed there is no way satellite imagery can be used to monitor leakage on a day to day basis.

Why? ...No..its not just that the spatial resolution won't be enough.

M: Where is 007 right now Q?

Q: ...(peering on towards a large screen)...Hmm...looks like he is skiing in Austria...his thermal trace is clearly visible..

Despite this fantasy land depiction of satellite imagery, there is no real-time feed of data in the real world of remote sensing and imagery analysis. Remote Sensing satellites, like the ones used by Google Maps and ISRO's Bhuvan, spin around the earth and image the same location every few weeks or so. They simply can't be used to monitor just one location for apps like water leakage.

Besides a lack of understanding of spatial and spectral resolution I think this is the biggest misunderstanding about satellite imagery that persists in popular imagination. Which is why the media keeps reporting that high resolution imagery can now be used to count the number of lions in Gir forest and to locate fish shoals.

So... can imagery to be used in applications like monitoring leakage from water pipes?

Yes, but their role will be as a reference to location. A city GIS will have several thematic layers...say roads, building footprints, green zones, cables and pipes all overlain on a geographic reference layer which could be a topographic map or a high resolution satellite image. The image being used as a backdrop may be six months or even a year old. The actual information about leakage is obtained from instruments like flow meters. The location of each flow meter along the pipes is known. This information by cross referencing the pipe layer with the imagery will help repair crews familiarize themselves with the exact location of the leaking pipe.

Thursday, January 7, 2010

Genes don't have real motives. Selfish in the term "selfish gene" really reflects the metaphorical motives of genes and not the real motives of individuals carrying those genes.

Ordinarily, different genes in the multicellular bodies of organisms co-operate. Such a system has evolved because in sexually reproducing multicellular organisms the reproductive fate of any gene depends on the successful reproduction of the individual. Genes in the somatic cells of the body, cells which form the body mass, can extend their lives only if a copy of themselves in the sex cells gets passed on. Co-operating to build successful bodies is the only way out.

But what if a gene is able bypass this system? What if a gene is able to unlink its reproduction from the reproduction of the individual?

Just such a situation has occurred in the spread of cancerous facial tumor in populations of the Tasmanian Devil - a carnivorous marsupial. Scientists working on these animals have identified a nerve cell type known as Schwann cells as the progenitor of this cancer which must have originated through mutations in one Schwann cell of one individual Tasmanian Devil.

Devils are aggressive creatures and they often bite each other
especially during mating. The cancer cells graft themselves on facial
tissue of the other individual and grow and spread. As cells divide, the bodies defense may kill some of these cells, but mutants among them which are better able to resist thus become more common. This is natural selection acting on this cell lineage. Within the lifetime of an individual devil, cancer cells divide hundreds of times. Cells in the nth generation would be different somewhat from their ancestral state. This is evolution, though not in the form we are familiar with or think of commonly. Ordinarily, this cancer cell lineage would die with the death of the individual. In this case, their evolution continues when they get grafted on another individual. The tumor gene thus
spreads through the population by bypassing the normal channels of
reproduction. The cancer cells have been able to successfully invade another body in this way
because there is very little genetic variation in the immune system of
the Tasmanian Devils. That may be because there are a small inbred
population. Immune cells don't recognize grafted cancer cells as foreign and don't reject them.

The mutant gene (s) responsible for this cancer can be thought of as a special type of a selfish gene. In a broader sense all genes are selfish since they "try" to maximize copies of themselves by competing against variations of themselves. Generally, the reproductive fate of the gene is tied to the reproductive fate of the individual and so genes cooperate to make bodies successful. However, in the more specific usage of the term, selfish genes may enhance their own reproduction by subverting the reproductive machinery of the cell and in the process causing harm to the population in the long run. During sexual reproduction any gene on average has a fifty percent chance of being passed on to the next generation. A selfish gene subverts these odds and ensures a more than even chance for copies of itself to be passed on.

In the case of the Tasmanian Devils, the "selfish gene" is not in the sex cells but is a somatic cell mutant.

We don't think of somatic cells as a separate life form. The cells that
make up our bodies are us. But occasionally as in the case of the
facial cancer in the Tasmanian Devils the us can morph into the other. Most cancerous cell types which rebel against the body don't have an extended evolutionary future. The cell lineage dies with the death of the individual. This particular cancer cell however, which was once part of the Tasmanian Devil is evolving into a parasite. It has developed a life of its own.

This situation illustrates several broader principles of evolution.

Firstly that evolution has no foresight. There is no long term benefit of the Tasmanian Devils that evolution is striving towards. Natural selection doesn't work for the benefit of the species. Evolution through natural selection is all about immediate advantage. Mutant cells have found a way to propagate independent of the body and because their life cycles operate quicker than that of an individual, selection will favor the spread of these cells regardless of whether that is harming Devil individuals and populations.

Second, it demonstrates that natural selection doesn't only act at the level of the individual. It can act on any entities which shows certain properties. If entities vary in certain traits, if these traits are heritable and if these
traits affect "fitness" i.e. they enable one variant to reproduce more
than the other then natural selection is off and running. In the
natural world these conditions are most familiarly met by whole
organisms but in principal they can be met by cells or genes within
cells.

In this case, selection is operating at two levels. At a lower level cells which contain the mutant gene are fitter than cells that don't contain this gene. But at a higher level individuals that don't contain this mutant gene are fitter than individuals that do. In most cases the "interests" of the gene and the individual coincide. Here, because their reproductive fates have been decoupled the relationship has turned antagonistic.

Finally, the study shows that the reconstruction of a complete evolutionary narrative requires thinking across the entire (or as much as possible) hierarchy of life. The so called division between reductionists and practitioners of "holistic" biology is and always has been a false dichotomy. Genes, cells, individuals, social behavior and population history all go to make the unfortunate story of the Tasmanian Devils more complete.

** Wishing readers coming to this post via Desipundit a very Happy New Year. If you missed my earlier announcement do note that my blog Reporting on a Revolution has been renamed Rapid Uplift. ...more in tune with the broad earth sciences / geology theme I write about. Thanks for your support.

Tuesday, January 5, 2010

Job opportunities should be plentiful for environmental scientists and especially for hydrologists. There were 8,100 hydrologist jobs in 2008, and employment should grow more than 18 percent by 2018. The government has stepped up environmental regulations and has begun cleaning up contaminated and hazardous waste sites—all efforts that increase the need for hydrological research. Competition for openings is limited by the small number of universities and colleges that offer degrees in hydrology.

The figures are for the United States but I would predict that a career to do with water holds a lot of promise in any country. This is not a new observation. Sometime back Science Careers carried a lengthy article on hydrogeology careers and called them "recession proof".

Population pressures, water reallocation challenges between rural and urban consumers, climate change and past mismanagement of water resources means there will be plenty of work for hydrologists and hydrogeologists for decades to come.

Begining with a foreshock of mag 6.5, a bigger shock of 7.2 and then a series of aftershocks of 5+; all within several hours of immense rumbling and shaking in the Solomon islands at the junction of the Australian plate and the Pacific plate. In the map below the plate boundary trends NW-SE just south of the islands.

The Solomon Islands earthquake of January 3, 2010, likely occurred
at the boundary between the Pacific and Australian plates, where the
Australian plate subducts beneath the Pacific towards the northeast at
a rate of approximately 95 mm/yr. The mechanism of the January 3rd
earthquake is consistent with its occurrence in relation to
underthrusting of the Australia plate beneath the Pacific plate, as
part of this subduction process.

The Solomon Islands arc as a whole experiences a very high level of
earthquake activity, and many shocks of magnitude 7 and larger have
been recorded since the early decades of the twentieth century. The
January 3rd, 2010 earthquake nucleated approximately 50 km to the
southeast of a M8.1 earthquake in April 2007, which with an associated
tsunami caused at least 50 fatalities and destroyed several coastal
villages on nearby islands. An M6.5 foreshock occurred less than one
hour before this main shock, in approximately the same location.

Monday, January 4, 2010

I got me a new blog name this new year. In a civil ceremony Reporting on a Revolution has been rechristened Rapid Uplift.

I think the new name has a restless dynamic geologyey feel to it. It is more in tune with the broad theme of my blog of a changing planet..being reshaped and re sculpted through geological processes and biological evolution. I have to admit that the focus of this blog has changed somewhat over the last two years. My initial purpose of keeping a tab on poor and sensationalistic science reporting especially by the Indian media prompted the blog title Reporting on a Revolution.

Over time though I have found myself writing more and more on geology related themes often not taking cues from media reports or without any intent to criticize media reporting but writing simply because I found a particular story interesting.

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ABOUT THIS BLOG

I am a Sedimentary Geologist. On Rapid Uplift I write mostly about topics within the geosciences, but sometimes on biological evolution and environmental issues. I like to travel and in my free time I teach 12 year old kids soccer and rugby.